nf-core_modules/tests/modules
2022-05-11 12:43:11 +02:00
..
abacas
abricate
adapterremoval Refactor adapterremoval (#1491) 2022-04-04 21:40:35 +02:00
adapterremovalfixprefix Add AdapterRemovalFixPrefix (#1424) 2022-03-21 11:26:12 +01:00
agrvate Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
allelecounter
amplify/predict
amps
amrfinderplus
antismash/antismashlitedownloaddatabases Update checksum in test.yml 2022-04-28 17:09:40 +02:00
arriba update md5sum 2022-05-09 15:19:16 +02:00
artic
ascat
assemblyscan
ataqv/ataqv
bakta
bamaligncleaner
bamcmp bamcmp (#1244) 2022-02-02 16:38:41 +00:00
bamtools
bamutil/trimbam
bandage/image
bbmap
bcftools
bclconvert
bedtools
biobambam
biscuit
bismark
blast
bowtie
bowtie2
bracken/bracken
busco remove 'auto' test 2022-05-06 13:33:27 +00:00
bwa
bwamem2
bwameth
cat
cellranger
centrifuge
checkm/lineagewf
chromap
clonalframeml
cmseq/polymut Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cnvkit/batch
cnvpytor combine multiple pytor 2022-05-05 23:59:12 +02:00
controlfreec
cooler
csvtk
custom
cutadapt
damageprofiler
dastool
dedup Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
deeparg
deeptools
deepvariant Update version & add intervals usage (#1214) 2022-01-17 16:40:31 +01:00
delly/call
diamond
dragmap
dragonflye
dshbio
ectyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
elprep
emmtyper
ensemblvep update ensemblvep and snpeff modules 2022-05-05 12:57:14 +02:00
expansionhunter
faqcs
fargene
fastani
fastp
fastqc
fastqscan
fasttree
fgbio
filtlong
flash
freebayes
gamma new module: GAMMA (#1532) 2022-04-23 10:12:06 -04:00
gatk4 fix datatest for stubs 2022-05-06 15:34:18 +02:00
genmap
genrich Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gffread Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
glnexus
graphmap2
gstama
gtdbtk/classifywf
gubbins
gunc
gunzip
hamronization
happy Split the module into two parts 2022-05-04 15:29:48 +02:00
hicap
hifiasm Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hisat2
hmmcopy
hmmer
homer
hpsuissero add module for hpsuisero (#1331) 2022-02-27 17:58:35 -07:00
ichorcna
idr
imputeme/vcftoprs
iqtree Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ismapper
isoseq3
ivar
jupyternotebook Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kaiju
kallisto/index
kallistobustools
kat/hist Change md5sum to contains 2022-05-10 15:13:25 +00:00
khmer/normalizebymedian
kleborate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
kraken2/kraken2
krona integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file 2022-05-05 13:51:41 +02:00
last
leehom Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
legsta
lima
lissero
lofreq
macrel/contigs Add new module macrel/contigs (#1109) 2021-12-09 13:17:50 +01:00
macs2/callpeak
mafft Add MAFFT module (#1351) 2022-02-28 00:40:24 -07:00
malt Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
maltextract
manta
mapdamage2
mash
mashtree
maxbin2
md5sum new module: md5sum 2022-05-06 09:20:40 +02:00
medaka
megahit
megan/rma2info
meningotype
meryl Merge branch 'master' into meryl_unionsum 2022-05-09 16:16:08 +02:00
metabat2
metaphlan3
methyldackel
minia
miniasm Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
minimap2
mlst Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mobsuite/recon add mobsuite_recon module (#1270) 2022-02-18 17:52:38 -07:00
mosdepth
motus/downloaddb
msisensor
msisensorpro
mtnucratio Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
multiqc
mummer
muscle Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nanolyse
nanoplot
ncbigenomedownload
nextclade
ngmaster
ngscheckmate/ncm
nucmer Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
optitype Add BAM indexes as input for optitype module. (#1388) 2022-03-15 17:02:40 +01:00
pairix
pairtools
panaroo/run
pangolin Bump Pangolin version to 3.1.20 (#1296) 2022-02-15 10:46:20 +00:00
paraclu
pbbam/pbmerge
pbccs Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
peddy
phantompeakqualtools
phyloflash
picard
pirate add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
plasmidid
plink
plink2
pmdtools/filter
porechop Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
preseq
prinseqplusplus
prodigal
prokka
pycoqc
pydamage
qcat Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
qualimap
quast
racon
rapidnj
rasusa
raven Raven assembler (#1087) 2022-02-01 11:47:01 +01:00
raxmlng
rgi/main
rmarkdownnotebook
roary
rsem
rseqc
rtgtools/vcfeval Small update on the output channels 2022-05-10 12:34:52 +02:00
salmon
samblaster
samtools Generalize Bam2Cram do either conversion 2022-05-09 15:22:54 +02:00
scoary
seacr/callpeak
seqkit
seqsero2
seqtk
sequenzautils
seqwish/induce
shasum added sha256sum 2022-05-06 10:28:14 +02:00
shigatyper make prettier 2022-04-21 12:55:56 -06:00
shovill
sistr
slimfastq
snapaligner fix tags 2022-05-06 18:57:17 +02:00
snpdists
snpeff
snpsift/split
snpsites
sourmash/sketch
spades Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
spatyper
sratools refactor: require settings input always 2022-05-10 12:29:42 +02:00
srst2/srst2
ssuissero
stadeniolib/scramble
staphopiasccmec
star
stranger add stubs for stranger (#1543) 2022-04-22 10:10:43 +02:00
strelka
stringtie
subread/featurecounts
svdb
tabix
tbprofiler/profile
tiddit
transdecoder
trimgalore Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ucsc
ultra/pipeline
umitools
unicycler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
untar
unzip
vardictjava
variantbam
vcfanno Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
vcflib/vcfuniq
vcftools
yara